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| Status |
Public on Sep 06, 2016 |
| Title |
DNase I 0h glucose |
| Sample type |
SRA |
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| Source name |
β-cell_DNase I 0h glucose
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| Organism |
Rattus norvegicus |
| Characteristics |
cell line: INS-1E
cell type: beta-cell
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| Treatment protocol |
Prior to exposure to high (25 mM) glucose, cells were preincubated with 5 mM glucose medium for 24 h. Time course experiments were performed in a reverse manner, i.e. medium was changed on all cells at time point 0 h, where after 25 mM glucose was added to the medium at consecutive time points and all cells were harvested at the 12 h time point.
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| Growth protocol |
INS-1E cells were cultured in RPMI 1640 w. 11 mM glucose supplemented with 5% Heat inactivated FCS, 50 uM β-MeOH, 1mM NaPyruvate, and 100 U/ml Penicilin + 100 mg/ml streptomycin. Cells were used between passages 60 and 90
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase-seq was performed on ~10 mill. nuclei essentially as described in (Siersbaek et al. 2011, EMBO J, 30: 1459-1472.).
RNA-, DNase-, and ChIP-seq libraries were constructed using PentAdapters (Pentabase) essentially as previously described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
processed data file: DNase_peakfile.txt
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| Data processing |
alignment: DNase-seq reads were mapped to rn5 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
peakdetection, quantification and visualization: Mapped DNAse-seq reads were peak detected and quantified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589). Tag directories were generated by calling makeTagDirectory (only including 1 tag pr bp, parameter: -tbp 1), and peak detection was performed using findPeaks -style factor (FDR ≤ 0. 1%). Peak locations and normalized counts (Pr. 10 M reads) for each condition are provided in DNAse_peakfile.txt. BedGraph files for visualization were generated using makeUCSCfile.
Genome_build: rn5
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| Submission date |
May 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
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| Phone |
+45 6550 2340
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| Organization name |
University of Southern Denmark
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| Department |
Biochemistry and Molecular Biology
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| Street address |
Campusvej 55
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| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platform ID |
GPL18404 |
| Series (1) |
| GSE81628 |
Integrative genomics outlines a biphasic glucose response and a ChREBP-RORγ axis regulating proliferation in β-cells |
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| Relations |
| BioSample |
SAMN05019626 |
| SRA |
SRX1774921 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2159998_DNase.5mM.bedGraph.gz |
63.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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